Multiple sequence alignment - TraesCS1D01G084200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G084200 chr1D 100.000 3943 0 0 1 3943 67860570 67864512 0.000000e+00 7282
1 TraesCS1D01G084200 chr1B 93.990 3178 124 34 488 3630 109210835 109213980 0.000000e+00 4748
2 TraesCS1D01G084200 chr1B 90.545 275 24 2 3622 3896 109215867 109216139 2.900000e-96 363
3 TraesCS1D01G084200 chr1B 91.803 244 18 1 216 459 109197972 109198213 4.880000e-89 339
4 TraesCS1D01G084200 chr1A 91.150 3435 169 57 1 3341 66174232 66177625 0.000000e+00 4534
5 TraesCS1D01G084200 chr1A 84.706 340 30 9 3344 3669 66178248 66178579 1.770000e-83 320
6 TraesCS1D01G084200 chr7D 81.277 235 41 2 3544 3778 22653918 22654149 1.870000e-43 187
7 TraesCS1D01G084200 chr7D 80.087 231 38 7 3550 3777 108621758 108621983 8.770000e-37 165
8 TraesCS1D01G084200 chr7D 81.319 182 25 8 3558 3734 616169719 616169542 5.310000e-29 139
9 TraesCS1D01G084200 chr7B 80.804 224 38 5 3554 3777 67836417 67836635 1.880000e-38 171


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G084200 chr1D 67860570 67864512 3942 False 7282.0 7282 100.0000 1 3943 1 chr1D.!!$F1 3942
1 TraesCS1D01G084200 chr1B 109210835 109216139 5304 False 2555.5 4748 92.2675 488 3896 2 chr1B.!!$F2 3408
2 TraesCS1D01G084200 chr1A 66174232 66178579 4347 False 2427.0 4534 87.9280 1 3669 2 chr1A.!!$F1 3668

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
171 196 0.178990 AAGGGTTTGAGGTGTCCAGC 60.179 55.0 0.00 0.00 0.00 4.85 F
828 875 0.388134 TTCGAGTTGGTGCGCTACTC 60.388 55.0 9.73 14.56 35.95 2.59 F
2372 2481 0.687354 TGTTGCAGAGGAGAAGGGAC 59.313 55.0 0.00 0.00 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1788 0.038310 TCCTCTGCTCCGAGAACAGA 59.962 55.0 0.0 2.76 38.09 3.41 R
2438 2547 0.591659 GGTTTCTTGCGAGGGTTGAC 59.408 55.0 0.0 0.00 0.00 3.18 R
3858 6501 0.366871 CGAGTTTTCAGATCACGGCG 59.633 55.0 4.8 4.80 0.00 6.46 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.179103 GATTTGAAATGGGCCTGGCG 60.179 55.000 13.40 0.00 0.00 5.69
75 76 4.169059 CACATATTGGGTGGGATTGAGA 57.831 45.455 0.00 0.00 32.65 3.27
81 82 0.548031 GGGTGGGATTGAGAGATGCA 59.452 55.000 0.00 0.00 0.00 3.96
82 83 1.476471 GGGTGGGATTGAGAGATGCAG 60.476 57.143 0.00 0.00 0.00 4.41
94 95 3.371965 AGAGATGCAGGCAAATCCAATT 58.628 40.909 0.00 0.00 37.29 2.32
96 97 2.835764 AGATGCAGGCAAATCCAATTGT 59.164 40.909 4.43 0.00 37.29 2.71
119 144 3.050089 TGGGTTGACTTTCTAGGTCCAA 58.950 45.455 0.00 0.00 33.22 3.53
124 149 2.288825 TGACTTTCTAGGTCCAACGCTG 60.289 50.000 0.00 0.00 33.22 5.18
138 163 2.426023 GCTGACTGGGTTGTCCGT 59.574 61.111 0.00 0.00 38.76 4.69
139 164 1.668151 GCTGACTGGGTTGTCCGTC 60.668 63.158 0.00 0.00 38.57 4.79
140 165 1.004918 CTGACTGGGTTGTCCGTCC 60.005 63.158 0.00 0.00 37.87 4.79
141 166 2.048503 GACTGGGTTGTCCGTCCG 60.049 66.667 0.00 0.00 38.76 4.79
151 176 2.242047 TGTCCGTCCGAACATTTGAA 57.758 45.000 0.00 0.00 0.00 2.69
160 185 4.506288 GTCCGAACATTTGAAAAGGGTTTG 59.494 41.667 0.00 0.00 0.00 2.93
162 187 4.744631 CCGAACATTTGAAAAGGGTTTGAG 59.255 41.667 8.42 0.40 0.00 3.02
167 192 4.729227 TTTGAAAAGGGTTTGAGGTGTC 57.271 40.909 0.00 0.00 0.00 3.67
169 194 2.024846 TGAAAAGGGTTTGAGGTGTCCA 60.025 45.455 0.00 0.00 0.00 4.02
171 196 0.178990 AAGGGTTTGAGGTGTCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
173 198 1.966451 GGTTTGAGGTGTCCAGCCG 60.966 63.158 0.00 0.00 0.00 5.52
176 201 0.759959 TTTGAGGTGTCCAGCCGTAA 59.240 50.000 0.00 0.00 0.00 3.18
193 218 2.671351 CGTAACGGACTTCTCACTGCAT 60.671 50.000 0.00 0.00 0.00 3.96
197 222 2.027745 ACGGACTTCTCACTGCATCAAT 60.028 45.455 0.00 0.00 0.00 2.57
202 227 2.408271 TCTCACTGCATCAATGGACC 57.592 50.000 0.00 0.00 0.00 4.46
310 344 4.261781 GCCGCCCGTCGTAGGTAG 62.262 72.222 0.00 0.00 36.19 3.18
334 368 2.743928 GGACGCAGGCCTTGACAG 60.744 66.667 0.00 0.00 0.00 3.51
379 416 2.207590 CACATACATGCATGTCGAGCT 58.792 47.619 34.54 12.88 41.97 4.09
385 422 2.690497 ACATGCATGTCGAGCTACTAGT 59.310 45.455 26.61 0.00 35.87 2.57
386 423 2.851805 TGCATGTCGAGCTACTAGTG 57.148 50.000 5.39 0.00 0.00 2.74
387 424 2.092323 TGCATGTCGAGCTACTAGTGT 58.908 47.619 5.39 0.00 0.00 3.55
400 437 1.557832 ACTAGTGTGTGTGTTGGTGGT 59.442 47.619 0.00 0.00 0.00 4.16
443 480 2.423577 GAGTGTCCGCAAATGTTACCT 58.576 47.619 0.00 0.00 0.00 3.08
445 482 1.877443 GTGTCCGCAAATGTTACCTGT 59.123 47.619 0.00 0.00 0.00 4.00
467 504 4.389576 GCGTGAAAGCTGCGGGTG 62.390 66.667 0.00 0.00 0.00 4.61
468 505 2.664851 CGTGAAAGCTGCGGGTGA 60.665 61.111 0.00 0.00 0.00 4.02
469 506 2.671177 CGTGAAAGCTGCGGGTGAG 61.671 63.158 0.00 0.00 0.00 3.51
470 507 1.301716 GTGAAAGCTGCGGGTGAGA 60.302 57.895 0.00 0.00 0.00 3.27
773 820 1.407575 GCTCTTCCTTAACTGCTCCCC 60.408 57.143 0.00 0.00 0.00 4.81
826 873 1.956620 GCTTCGAGTTGGTGCGCTAC 61.957 60.000 9.73 5.08 0.00 3.58
827 874 0.388649 CTTCGAGTTGGTGCGCTACT 60.389 55.000 9.73 6.86 0.00 2.57
828 875 0.388134 TTCGAGTTGGTGCGCTACTC 60.388 55.000 9.73 14.56 35.95 2.59
992 1043 3.916172 CCGTCGTTTATATATCCACACCG 59.084 47.826 0.00 0.00 0.00 4.94
1017 1074 2.076863 GGGATGTGAGTTTCTTGACGG 58.923 52.381 0.00 0.00 0.00 4.79
1018 1075 1.464997 GGATGTGAGTTTCTTGACGGC 59.535 52.381 0.00 0.00 0.00 5.68
1019 1076 2.417719 GATGTGAGTTTCTTGACGGCT 58.582 47.619 0.00 0.00 0.00 5.52
1021 1078 1.138069 TGTGAGTTTCTTGACGGCTGA 59.862 47.619 0.00 0.00 0.00 4.26
1036 1096 0.868406 GCTGACCGTGTTCTTCCTTG 59.132 55.000 0.00 0.00 0.00 3.61
1051 1112 5.755849 TCTTCCTTGTCTTCTTGGTTCTTT 58.244 37.500 0.00 0.00 0.00 2.52
1474 1545 4.916293 GATGCCGGAGCGCCATCA 62.916 66.667 5.05 3.52 44.31 3.07
1665 1754 0.879765 AACAAGTCCGTCGAGTCGAT 59.120 50.000 19.75 0.00 38.42 3.59
1747 1836 2.989639 CATCCGCCCAAGGAGTCA 59.010 61.111 0.00 0.00 44.55 3.41
1849 1938 2.032681 AGACTGCAACCGGAAGCC 59.967 61.111 9.46 0.00 0.00 4.35
1896 1985 2.147387 AACCGGAAGTGAGGGCTGT 61.147 57.895 9.46 0.00 0.00 4.40
1924 2013 1.408683 CCCCAGAGATTGCAATCGGAA 60.409 52.381 28.88 0.00 40.35 4.30
2068 2157 2.627737 GGACGACGAGGTGAGCACT 61.628 63.158 0.00 0.00 0.00 4.40
2106 2211 3.312421 GCAGTACTGTGCTTCTTGTTTCA 59.688 43.478 23.44 0.00 40.54 2.69
2107 2212 4.023707 GCAGTACTGTGCTTCTTGTTTCAT 60.024 41.667 23.44 0.00 40.54 2.57
2108 2213 5.446709 CAGTACTGTGCTTCTTGTTTCATG 58.553 41.667 15.06 0.00 0.00 3.07
2267 2372 5.173673 CGATCCCGAATGCACAAAATAAATG 59.826 40.000 0.00 0.00 38.22 2.32
2268 2373 5.398603 TCCCGAATGCACAAAATAAATGT 57.601 34.783 0.00 0.00 0.00 2.71
2339 2448 7.633789 TCCTTCTTGGAAGATAGCTAAAATGT 58.366 34.615 0.00 0.00 42.94 2.71
2372 2481 0.687354 TGTTGCAGAGGAGAAGGGAC 59.313 55.000 0.00 0.00 0.00 4.46
2438 2547 0.231279 GCAACAAGGTACACGACACG 59.769 55.000 0.00 0.00 0.00 4.49
2501 2612 4.810491 GCACAAAGTGACATCCAATGTTTT 59.190 37.500 0.58 0.00 45.03 2.43
2502 2613 5.982516 GCACAAAGTGACATCCAATGTTTTA 59.017 36.000 0.58 0.00 45.03 1.52
2516 2627 7.999679 TCCAATGTTTTATGGTGATGAAGATC 58.000 34.615 0.00 0.00 37.94 2.75
3045 3156 2.331098 CTGCGGCAAAACGAAGCA 59.669 55.556 3.44 0.00 31.89 3.91
3193 3304 4.382470 GCAGTACTCAATCCTGACATGTCT 60.382 45.833 25.55 3.34 0.00 3.41
3198 3309 4.115516 CTCAATCCTGACATGTCTTACCG 58.884 47.826 25.55 10.62 0.00 4.02
3201 3312 0.806102 CCTGACATGTCTTACCGCCG 60.806 60.000 25.55 5.07 0.00 6.46
3213 3324 3.565063 TCTTACCGCCGTTTTTAAAGCTT 59.435 39.130 0.00 0.00 0.00 3.74
3231 3346 1.730451 TTCGTCCGCCGCTCATGATA 61.730 55.000 0.00 0.00 36.19 2.15
3261 3376 1.823295 GCGGGCAGGAGTCAATCTA 59.177 57.895 0.00 0.00 0.00 1.98
3342 3457 2.825836 GGCTCGGGCAGTCCATTG 60.826 66.667 10.74 0.00 40.87 2.82
3354 4089 3.881688 GCAGTCCATTGCTTATCATCAGT 59.118 43.478 0.00 0.00 40.89 3.41
3376 4111 2.579684 CTTGTGGGAGCGTAGGAGCC 62.580 65.000 0.00 0.00 38.01 4.70
3448 4192 2.437359 CGGGGAGCAGGAGCAAAG 60.437 66.667 0.00 0.00 45.49 2.77
3468 4212 1.154035 GCGCAAAGGGTTTGGATCG 60.154 57.895 0.30 0.00 40.94 3.69
3483 4227 2.151202 GGATCGAGCCAACTGAAAACA 58.849 47.619 16.44 0.00 0.00 2.83
3492 4236 6.348458 CGAGCCAACTGAAAACATGAGAATAA 60.348 38.462 0.00 0.00 0.00 1.40
3493 4237 6.917533 AGCCAACTGAAAACATGAGAATAAG 58.082 36.000 0.00 0.00 0.00 1.73
3519 4266 4.579454 ACATAAGATTGACATGGCATGC 57.421 40.909 26.70 18.94 0.00 4.06
3531 4278 2.721425 TGGCATGCTCATCTCAATCA 57.279 45.000 18.92 0.00 0.00 2.57
3532 4279 3.007473 TGGCATGCTCATCTCAATCAA 57.993 42.857 18.92 0.00 0.00 2.57
3533 4280 2.686405 TGGCATGCTCATCTCAATCAAC 59.314 45.455 18.92 0.00 0.00 3.18
3535 4282 4.132336 GGCATGCTCATCTCAATCAACTA 58.868 43.478 18.92 0.00 0.00 2.24
3536 4283 4.760715 GGCATGCTCATCTCAATCAACTAT 59.239 41.667 18.92 0.00 0.00 2.12
3537 4284 5.936372 GGCATGCTCATCTCAATCAACTATA 59.064 40.000 18.92 0.00 0.00 1.31
3538 4285 6.092396 GGCATGCTCATCTCAATCAACTATAG 59.908 42.308 18.92 0.00 0.00 1.31
3539 4286 6.092396 GCATGCTCATCTCAATCAACTATAGG 59.908 42.308 11.37 0.00 0.00 2.57
3542 4289 6.552725 TGCTCATCTCAATCAACTATAGGAGT 59.447 38.462 4.43 0.00 41.56 3.85
3544 4291 8.748412 GCTCATCTCAATCAACTATAGGAGTAT 58.252 37.037 4.43 0.00 37.44 2.12
3578 4325 3.747854 TTGGCTTGTTTGATTGCATCA 57.252 38.095 0.00 0.00 37.55 3.07
3597 4345 9.425248 TTGCATCATAGAAGAAATAAGGGATTT 57.575 29.630 0.00 0.00 40.62 2.17
3661 6304 9.379791 AGAAATAGTACAAAGAAATCGTTAGGG 57.620 33.333 0.00 0.00 0.00 3.53
3670 6313 8.638873 ACAAAGAAATCGTTAGGGAAAATTCTT 58.361 29.630 0.00 0.00 37.45 2.52
3671 6314 8.915654 CAAAGAAATCGTTAGGGAAAATTCTTG 58.084 33.333 0.00 0.00 36.37 3.02
3672 6315 7.761038 AGAAATCGTTAGGGAAAATTCTTGT 57.239 32.000 0.00 0.00 0.00 3.16
3673 6316 7.593825 AGAAATCGTTAGGGAAAATTCTTGTG 58.406 34.615 0.00 0.00 0.00 3.33
3755 6398 6.531021 TCCTTCAAAGTTCCTACGAAAATCT 58.469 36.000 0.00 0.00 0.00 2.40
3797 6440 1.289694 CTTTTGCTCCATTGGCGCA 59.710 52.632 16.19 16.19 41.96 6.09
3798 6441 1.006337 TTTTGCTCCATTGGCGCAC 60.006 52.632 19.57 0.00 43.43 5.34
3848 6491 3.306294 CCTCAAGAATTTTGAAGGGGCAC 60.306 47.826 5.12 0.00 0.00 5.01
3877 6520 0.366871 CGCCGTGATCTGAAAACTCG 59.633 55.000 0.00 0.00 0.00 4.18
3878 6521 1.429463 GCCGTGATCTGAAAACTCGT 58.571 50.000 0.00 0.00 0.00 4.18
3880 6523 2.991190 GCCGTGATCTGAAAACTCGTAA 59.009 45.455 0.00 0.00 0.00 3.18
3884 6527 4.029198 CGTGATCTGAAAACTCGTAACTCG 59.971 45.833 0.00 0.00 41.41 4.18
3896 6539 6.560253 ACTCGTAACTCGTTAGGTAGAAAA 57.440 37.500 8.74 0.00 40.80 2.29
3897 6540 6.374578 ACTCGTAACTCGTTAGGTAGAAAAC 58.625 40.000 8.74 0.00 40.80 2.43
3898 6541 6.205658 ACTCGTAACTCGTTAGGTAGAAAACT 59.794 38.462 8.74 0.00 40.80 2.66
3899 6542 6.603095 TCGTAACTCGTTAGGTAGAAAACTC 58.397 40.000 8.74 0.00 40.80 3.01
3900 6543 5.506138 CGTAACTCGTTAGGTAGAAAACTCG 59.494 44.000 2.30 0.00 34.52 4.18
3901 6544 5.444663 AACTCGTTAGGTAGAAAACTCGT 57.555 39.130 0.00 0.00 0.00 4.18
3902 6545 6.560253 AACTCGTTAGGTAGAAAACTCGTA 57.440 37.500 0.00 0.00 0.00 3.43
3903 6546 6.560253 ACTCGTTAGGTAGAAAACTCGTAA 57.440 37.500 0.00 0.00 0.00 3.18
3904 6547 6.374578 ACTCGTTAGGTAGAAAACTCGTAAC 58.625 40.000 0.00 0.00 32.63 2.50
3905 6548 6.205658 ACTCGTTAGGTAGAAAACTCGTAACT 59.794 38.462 0.00 0.00 33.30 2.24
3906 6549 6.603095 TCGTTAGGTAGAAAACTCGTAACTC 58.397 40.000 0.00 0.00 33.30 3.01
3907 6550 5.506138 CGTTAGGTAGAAAACTCGTAACTCG 59.494 44.000 0.00 0.00 41.41 4.18
3908 6551 6.374578 GTTAGGTAGAAAACTCGTAACTCGT 58.625 40.000 0.00 0.00 40.80 4.18
3909 6552 5.444663 AGGTAGAAAACTCGTAACTCGTT 57.555 39.130 0.00 0.00 40.80 3.85
3910 6553 6.560253 AGGTAGAAAACTCGTAACTCGTTA 57.440 37.500 0.00 0.00 40.80 3.18
3911 6554 6.606768 AGGTAGAAAACTCGTAACTCGTTAG 58.393 40.000 0.00 0.00 40.80 2.34
3912 6555 5.797434 GGTAGAAAACTCGTAACTCGTTAGG 59.203 44.000 3.75 3.75 40.80 2.69
3913 6556 5.444663 AGAAAACTCGTAACTCGTTAGGT 57.555 39.130 8.74 0.00 40.80 3.08
3914 6557 6.560253 AGAAAACTCGTAACTCGTTAGGTA 57.440 37.500 8.74 0.00 40.80 3.08
3915 6558 6.606768 AGAAAACTCGTAACTCGTTAGGTAG 58.393 40.000 8.74 7.79 40.80 3.18
3916 6559 6.428159 AGAAAACTCGTAACTCGTTAGGTAGA 59.572 38.462 8.74 0.00 40.80 2.59
3917 6560 6.560253 AAACTCGTAACTCGTTAGGTAGAA 57.440 37.500 8.74 0.00 40.80 2.10
3918 6561 6.560253 AACTCGTAACTCGTTAGGTAGAAA 57.440 37.500 8.74 0.00 40.80 2.52
3919 6562 6.749923 ACTCGTAACTCGTTAGGTAGAAAT 57.250 37.500 8.74 0.00 40.80 2.17
3920 6563 7.150783 ACTCGTAACTCGTTAGGTAGAAATT 57.849 36.000 8.74 0.00 40.80 1.82
3921 6564 7.025963 ACTCGTAACTCGTTAGGTAGAAATTG 58.974 38.462 8.74 0.00 40.80 2.32
3922 6565 5.801947 TCGTAACTCGTTAGGTAGAAATTGC 59.198 40.000 8.74 0.00 40.80 3.56
3923 6566 5.574055 CGTAACTCGTTAGGTAGAAATTGCA 59.426 40.000 2.30 0.00 34.52 4.08
3924 6567 6.255020 CGTAACTCGTTAGGTAGAAATTGCAT 59.745 38.462 0.00 0.00 34.52 3.96
3925 6568 6.422776 AACTCGTTAGGTAGAAATTGCATG 57.577 37.500 0.00 0.00 0.00 4.06
3926 6569 5.730550 ACTCGTTAGGTAGAAATTGCATGA 58.269 37.500 0.00 0.00 0.00 3.07
3927 6570 6.170506 ACTCGTTAGGTAGAAATTGCATGAA 58.829 36.000 0.00 0.00 0.00 2.57
3928 6571 6.313905 ACTCGTTAGGTAGAAATTGCATGAAG 59.686 38.462 0.00 0.00 0.00 3.02
3929 6572 6.403049 TCGTTAGGTAGAAATTGCATGAAGA 58.597 36.000 0.00 0.00 0.00 2.87
3930 6573 6.312918 TCGTTAGGTAGAAATTGCATGAAGAC 59.687 38.462 0.00 0.00 0.00 3.01
3931 6574 6.092122 CGTTAGGTAGAAATTGCATGAAGACA 59.908 38.462 0.00 0.00 0.00 3.41
3932 6575 7.201644 CGTTAGGTAGAAATTGCATGAAGACAT 60.202 37.037 0.00 0.00 37.19 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.108168 TCTCTCCGAATCGTTCCCAAT 58.892 47.619 0.82 0.00 0.00 3.16
11 12 4.572389 CCATTTCAAATCTCTCCGAATCGT 59.428 41.667 0.82 0.00 0.00 3.73
17 18 1.678101 GGCCCATTTCAAATCTCTCCG 59.322 52.381 0.00 0.00 0.00 4.63
70 71 2.291089 TGGATTTGCCTGCATCTCTCAA 60.291 45.455 0.00 0.00 37.63 3.02
71 72 1.282738 TGGATTTGCCTGCATCTCTCA 59.717 47.619 0.00 0.00 37.63 3.27
72 73 2.048444 TGGATTTGCCTGCATCTCTC 57.952 50.000 0.00 0.00 37.63 3.20
73 74 2.519771 TTGGATTTGCCTGCATCTCT 57.480 45.000 0.00 0.00 37.63 3.10
74 75 3.118884 ACAATTGGATTTGCCTGCATCTC 60.119 43.478 10.83 0.00 37.63 2.75
75 76 2.835764 ACAATTGGATTTGCCTGCATCT 59.164 40.909 10.83 0.00 37.63 2.90
94 95 4.457466 GACCTAGAAAGTCAACCCAAACA 58.543 43.478 0.00 0.00 34.27 2.83
96 97 3.460340 TGGACCTAGAAAGTCAACCCAAA 59.540 43.478 0.00 0.00 35.89 3.28
119 144 2.426023 GGACAACCCAGTCAGCGT 59.574 61.111 0.00 0.00 40.29 5.07
124 149 2.048503 CGGACGGACAACCCAGTC 60.049 66.667 0.00 0.00 37.57 3.51
138 163 4.402793 TCAAACCCTTTTCAAATGTTCGGA 59.597 37.500 0.00 0.00 0.00 4.55
139 164 4.688021 TCAAACCCTTTTCAAATGTTCGG 58.312 39.130 0.00 0.00 0.00 4.30
140 165 4.744631 CCTCAAACCCTTTTCAAATGTTCG 59.255 41.667 0.00 0.00 0.00 3.95
141 166 5.523552 CACCTCAAACCCTTTTCAAATGTTC 59.476 40.000 0.00 0.00 0.00 3.18
151 176 1.754201 GCTGGACACCTCAAACCCTTT 60.754 52.381 0.00 0.00 0.00 3.11
160 185 1.445582 CGTTACGGCTGGACACCTC 60.446 63.158 0.00 0.00 0.00 3.85
162 187 2.433664 CCGTTACGGCTGGACACC 60.434 66.667 11.93 0.00 41.17 4.16
173 198 2.433868 TGCAGTGAGAAGTCCGTTAC 57.566 50.000 0.00 0.00 0.00 2.50
176 201 0.969149 TGATGCAGTGAGAAGTCCGT 59.031 50.000 0.00 0.00 0.00 4.69
329 363 2.358615 GCATGTGTCCGGCTGTCA 60.359 61.111 0.00 0.00 0.00 3.58
334 368 4.197498 GGCATGCATGTGTCCGGC 62.197 66.667 26.79 11.23 0.00 6.13
371 408 2.225727 CACACACACTAGTAGCTCGACA 59.774 50.000 0.00 0.00 0.00 4.35
379 416 2.767394 ACCACCAACACACACACTAGTA 59.233 45.455 0.00 0.00 0.00 1.82
385 422 0.678366 GTCCACCACCAACACACACA 60.678 55.000 0.00 0.00 0.00 3.72
386 423 1.381165 GGTCCACCACCAACACACAC 61.381 60.000 0.00 0.00 45.98 3.82
387 424 1.077357 GGTCCACCACCAACACACA 60.077 57.895 0.00 0.00 45.98 3.72
400 437 2.122324 TTTCCTCCCACCGGTCCA 60.122 61.111 2.59 0.00 0.00 4.02
443 480 1.664649 CAGCTTTCACGCGAGGACA 60.665 57.895 15.93 1.76 34.40 4.02
445 482 2.738521 GCAGCTTTCACGCGAGGA 60.739 61.111 15.93 7.21 34.40 3.71
465 502 2.167398 TTGCACGGCTAGGGTCTCAC 62.167 60.000 0.00 0.00 0.00 3.51
466 503 1.888436 CTTGCACGGCTAGGGTCTCA 61.888 60.000 0.00 0.00 0.00 3.27
467 504 1.153549 CTTGCACGGCTAGGGTCTC 60.154 63.158 0.00 0.00 0.00 3.36
468 505 1.608717 CTCTTGCACGGCTAGGGTCT 61.609 60.000 7.28 0.00 32.69 3.85
469 506 1.153549 CTCTTGCACGGCTAGGGTC 60.154 63.158 7.28 0.00 32.69 4.46
470 507 1.192146 TTCTCTTGCACGGCTAGGGT 61.192 55.000 6.99 0.00 33.84 4.34
473 510 2.086054 ACTTTCTCTTGCACGGCTAG 57.914 50.000 0.00 0.00 33.07 3.42
474 511 2.543777 AACTTTCTCTTGCACGGCTA 57.456 45.000 0.00 0.00 0.00 3.93
475 512 1.334869 CAAACTTTCTCTTGCACGGCT 59.665 47.619 0.00 0.00 0.00 5.52
476 513 1.600413 CCAAACTTTCTCTTGCACGGC 60.600 52.381 0.00 0.00 0.00 5.68
715 762 1.063006 CGTCGCCATTGATGCCAAG 59.937 57.895 0.00 0.00 35.48 3.61
773 820 3.490759 GATGCGCGTGTGTGAGGG 61.491 66.667 6.97 0.00 0.00 4.30
826 873 2.041405 GGGGTGGAGGAGGAGGAG 60.041 72.222 0.00 0.00 0.00 3.69
827 874 2.540910 AGGGGTGGAGGAGGAGGA 60.541 66.667 0.00 0.00 0.00 3.71
828 875 2.041405 GAGGGGTGGAGGAGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
992 1043 1.749258 GAAACTCACATCCCCGGCC 60.749 63.158 0.00 0.00 0.00 6.13
1017 1074 0.868406 CAAGGAAGAACACGGTCAGC 59.132 55.000 0.00 0.00 0.00 4.26
1018 1075 2.135933 GACAAGGAAGAACACGGTCAG 58.864 52.381 0.00 0.00 0.00 3.51
1019 1076 1.760613 AGACAAGGAAGAACACGGTCA 59.239 47.619 0.00 0.00 0.00 4.02
1021 1078 2.434702 AGAAGACAAGGAAGAACACGGT 59.565 45.455 0.00 0.00 0.00 4.83
1027 1087 5.373812 AGAACCAAGAAGACAAGGAAGAA 57.626 39.130 0.00 0.00 0.00 2.52
1036 1096 4.435651 CGGCGAATAAAGAACCAAGAAGAC 60.436 45.833 0.00 0.00 0.00 3.01
1051 1112 0.602638 CTAGCAATGGCCGGCGAATA 60.603 55.000 22.54 7.10 42.56 1.75
1111 1179 3.188100 ATCACGCACACGCCATCG 61.188 61.111 0.00 0.00 45.53 3.84
1160 1231 2.296365 CCCAGAGCAGCTCCTCCAA 61.296 63.158 19.40 0.00 32.17 3.53
1399 1470 3.409570 GGGAAACAAGGTGGAGAAGTAC 58.590 50.000 0.00 0.00 0.00 2.73
1474 1545 4.280494 ACCGCTGCGTGAGACGTT 62.280 61.111 21.59 0.00 44.73 3.99
1647 1736 0.168348 CATCGACTCGACGGACTTGT 59.832 55.000 2.53 0.00 39.18 3.16
1699 1788 0.038310 TCCTCTGCTCCGAGAACAGA 59.962 55.000 0.00 2.76 38.09 3.41
1732 1821 3.319198 GGTGACTCCTTGGGCGGA 61.319 66.667 0.00 0.00 0.00 5.54
1758 1847 4.570663 GAGGACGGGATGCGGACG 62.571 72.222 0.00 0.00 0.00 4.79
2068 2157 2.586635 GCGTTCGTGGTGTGTCCA 60.587 61.111 0.00 0.00 45.01 4.02
2106 2211 4.860907 GCAGATTGCGTTTGAGATTTTCAT 59.139 37.500 0.00 0.00 31.95 2.57
2107 2212 4.229096 GCAGATTGCGTTTGAGATTTTCA 58.771 39.130 0.00 0.00 31.71 2.69
2108 2213 3.609807 GGCAGATTGCGTTTGAGATTTTC 59.390 43.478 0.00 0.00 46.21 2.29
2267 2372 1.666888 CCACTTCGGTGTACGGTGTAC 60.667 57.143 0.22 0.22 43.91 2.90
2268 2373 0.597568 CCACTTCGGTGTACGGTGTA 59.402 55.000 0.00 0.00 43.91 2.90
2336 2445 5.539979 TGCAACAGCAATTTCATACAACAT 58.460 33.333 0.00 0.00 34.85 2.71
2339 2448 5.450592 TCTGCAACAGCAATTTCATACAA 57.549 34.783 0.00 0.00 37.91 2.41
2372 2481 1.256376 CGCATCTTCTCGTTGATTCGG 59.744 52.381 0.00 0.00 0.00 4.30
2438 2547 0.591659 GGTTTCTTGCGAGGGTTGAC 59.408 55.000 0.00 0.00 0.00 3.18
2456 2566 5.149977 GCTCTTGTCAAAGATTTTTCGAGG 58.850 41.667 0.00 0.00 41.60 4.63
2501 2612 4.740634 GCCTTGTCGATCTTCATCACCATA 60.741 45.833 0.00 0.00 0.00 2.74
2502 2613 3.801698 CCTTGTCGATCTTCATCACCAT 58.198 45.455 0.00 0.00 0.00 3.55
2963 3074 0.309302 CTACAGAGCCAGATCGACCG 59.691 60.000 0.00 0.00 0.00 4.79
3193 3304 3.606615 CGAAGCTTTAAAAACGGCGGTAA 60.607 43.478 13.24 0.99 0.00 2.85
3198 3309 2.313234 GGACGAAGCTTTAAAAACGGC 58.687 47.619 0.00 0.00 0.00 5.68
3201 3312 2.313234 GGCGGACGAAGCTTTAAAAAC 58.687 47.619 0.00 0.00 34.52 2.43
3242 3357 2.016393 TAGATTGACTCCTGCCCGCG 62.016 60.000 0.00 0.00 0.00 6.46
3261 3376 3.179830 CGAACAGTGCTCGCTATACTTT 58.820 45.455 2.54 0.00 0.00 2.66
3300 3415 2.282040 GCTCAAGCTGCCACCAGT 60.282 61.111 0.00 0.00 41.26 4.00
3341 3456 3.441222 CCACAAGCAACTGATGATAAGCA 59.559 43.478 0.00 0.00 0.00 3.91
3342 3457 3.181493 CCCACAAGCAACTGATGATAAGC 60.181 47.826 0.00 0.00 0.00 3.09
3354 4089 1.003839 CCTACGCTCCCACAAGCAA 60.004 57.895 0.00 0.00 42.62 3.91
3376 4111 3.976701 ATCTTTGGCCCCGACGCAG 62.977 63.158 0.00 0.00 0.00 5.18
3448 4192 2.225791 GATCCAAACCCTTTGCGCCC 62.226 60.000 4.18 0.00 39.31 6.13
3468 4212 4.836125 TTCTCATGTTTTCAGTTGGCTC 57.164 40.909 0.00 0.00 0.00 4.70
3492 4236 7.230849 TGCCATGTCAATCTTATGTTTTTCT 57.769 32.000 0.00 0.00 0.00 2.52
3493 4237 7.464977 GCATGCCATGTCAATCTTATGTTTTTC 60.465 37.037 6.36 0.00 0.00 2.29
3508 4255 1.963172 TGAGATGAGCATGCCATGTC 58.037 50.000 25.83 25.83 35.59 3.06
3635 6278 9.379791 CCCTAACGATTTCTTTGTACTATTTCT 57.620 33.333 0.00 0.00 0.00 2.52
3742 6385 8.296713 CCTTTGATTCAAAAGATTTTCGTAGGA 58.703 33.333 12.62 0.00 39.12 2.94
3743 6386 8.296713 TCCTTTGATTCAAAAGATTTTCGTAGG 58.703 33.333 12.62 6.23 39.12 3.18
3755 6398 4.772100 CCTTAGGGCTCCTTTGATTCAAAA 59.228 41.667 12.62 0.00 34.61 2.44
3797 6440 1.041447 ACGCTACGCCCATAGAAGGT 61.041 55.000 0.00 0.00 0.00 3.50
3798 6441 0.956633 TACGCTACGCCCATAGAAGG 59.043 55.000 0.00 0.00 0.00 3.46
3820 6463 5.221501 CCCTTCAAAATTCTTGAGGCTTTCA 60.222 40.000 0.00 0.00 0.00 2.69
3821 6464 5.233225 CCCTTCAAAATTCTTGAGGCTTTC 58.767 41.667 0.00 0.00 0.00 2.62
3858 6501 0.366871 CGAGTTTTCAGATCACGGCG 59.633 55.000 4.80 4.80 0.00 6.46
3860 6503 4.235360 AGTTACGAGTTTTCAGATCACGG 58.765 43.478 0.00 0.00 0.00 4.94
3877 6520 6.374578 ACGAGTTTTCTACCTAACGAGTTAC 58.625 40.000 0.00 0.00 0.00 2.50
3878 6521 6.560253 ACGAGTTTTCTACCTAACGAGTTA 57.440 37.500 0.00 0.00 0.00 2.24
3880 6523 6.205658 AGTTACGAGTTTTCTACCTAACGAGT 59.794 38.462 0.00 0.00 0.00 4.18
3884 6527 6.374578 ACGAGTTACGAGTTTTCTACCTAAC 58.625 40.000 0.00 0.00 45.77 2.34
3896 6539 6.749923 ATTTCTACCTAACGAGTTACGAGT 57.250 37.500 0.00 0.00 45.77 4.18
3897 6540 6.020837 GCAATTTCTACCTAACGAGTTACGAG 60.021 42.308 0.00 0.00 45.77 4.18
3898 6541 5.801947 GCAATTTCTACCTAACGAGTTACGA 59.198 40.000 0.00 0.00 45.77 3.43
3900 6543 6.956299 TGCAATTTCTACCTAACGAGTTAC 57.044 37.500 0.00 0.00 0.00 2.50
3901 6544 7.324935 TCATGCAATTTCTACCTAACGAGTTA 58.675 34.615 0.00 0.00 0.00 2.24
3902 6545 6.170506 TCATGCAATTTCTACCTAACGAGTT 58.829 36.000 0.00 0.00 0.00 3.01
3903 6546 5.730550 TCATGCAATTTCTACCTAACGAGT 58.269 37.500 0.00 0.00 0.00 4.18
3904 6547 6.535150 TCTTCATGCAATTTCTACCTAACGAG 59.465 38.462 0.00 0.00 0.00 4.18
3905 6548 6.312918 GTCTTCATGCAATTTCTACCTAACGA 59.687 38.462 0.00 0.00 0.00 3.85
3906 6549 6.092122 TGTCTTCATGCAATTTCTACCTAACG 59.908 38.462 0.00 0.00 0.00 3.18
3907 6550 7.377766 TGTCTTCATGCAATTTCTACCTAAC 57.622 36.000 0.00 0.00 0.00 2.34
3908 6551 7.988737 CATGTCTTCATGCAATTTCTACCTAA 58.011 34.615 0.00 0.00 43.66 2.69
3909 6552 7.558161 CATGTCTTCATGCAATTTCTACCTA 57.442 36.000 0.00 0.00 43.66 3.08
3910 6553 6.446781 CATGTCTTCATGCAATTTCTACCT 57.553 37.500 0.00 0.00 43.66 3.08


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.